Predictive modelling of response to neoadjuvant therapy in HER2+ breast cancer

HER2-positive (HER2+) breast cancer accounts for 20–25% of all breast cancers. Predictive biomarkers of neoadjuvant therapy response are needed to better identify patients with early stage disease who may benefit from tailored treatments in the adjuvant setting. As part of the TCHL phase-II clinical trial (ICORG10–05/NCT01485926) whole exome DNA sequencing was carried out on normal-tumour pairs collected from 22 patients. Here we report predictive modelling of neoadjuvant therapy response using clinicopathological and genomic features of pre-treatment tumour biopsies identified age, estrogen receptor (ER) status and level of immune cell infiltration may together be important for predicting response. Clonal evolution analysis of longitudinally collected tumour samples show subclonal diversity and dynamics are evident with potential therapy resistant subclones detected. The sources of greater pre-treatment immunogenicity associated with a pathological complete response is largely unexplored in HER2+ tumours. However, here we point to the possibility of APOBEC associated mutagenesis, specifically in the ER-neg/HER2+ subtype as a potential mediator of this immunogenic phenotype.

Supplementary Figure 1.Two step FACETS-CNVKit somatic copy number calling approach.(a) Graphical summary of the two-step FACETS-CNVKit somatic copy number calling approach (b) Scatterplots and corresponding Spearman correlation coefficient (R) quantify the relationship between CNVKit derived discrete copy number (CN) call (y-axis) and FACETS derived total copy number (TCN) call (x-axis) for a set of known breast cancer driver genes including ERBB2 (HER2) (labelled) for tumour samples (from left-right, top-bottom) flagged using the somatic copy number calling approach described in (a).Spearman Rho Rank correlation statistical test P<0.05.

MYC chr8 ERBB2(HER2) chr17
Supplementary Figure 2. Manual review of somatic copy number calls using IGV.From the Integrated Genome Viewer (IGV) FACETS derived medium copy number log ratio value ( Top panel; red: copy number gain or amplification while blue : copy number loss or deletion for the segment) from joint segmentation of total and allele specific copy number calling in the ERRB2 (HER2) gene on chromosome 17 and MYC oncogene on chromosome 8 for flagged tumour samples.Bottom panel shows the sequencing coverage over captured DNA regions including exons for the ERBB2 (HER2) and MYC oncogenes.IGV Reference human genome track GRCh38.
signature profiling using deconstructSigs.(a) Overview of mutational signature workflow using deconstructSigs.(b) Stacked barchart of the relative contribution [0-1] of COSMIC reference mutational signatures detected in each pre-treatment tumour biopsy sample (n=22) (leftright) from the HER2+ TCHL WXS cohort.(c) Barchart shows frequency of COSMIC reference mutational signatures (top-bottom) across all pre-treatment biopsy samples (n=22).Dashed line indicates 2 or more samples.(e) Boxplots show the distribution of relative contribution values of frequent COSMIC reference signatures (present in >2 samples) in pCR (n=9; white) compared to RD (n=13; grey) classified tumours (Wilcox Test P<0.05).Horizontal lines in the box plots denote the lower quartile (Q1), median and upper quartile (Q3).The box bounds the interquartile range (IQR = Q3 − Q1) with the whiskers denoting 1.5 x IQR.Pre-treatment biopsy sample (n=22)

Fisher
of HER2+ cases annotated by APOBEC associated mutational signature status according to tumour response status.(a) Stacked barchart shows the proportion of patients with HER2+ breast cancer who had a pathological complete response (pCR; N=18) or residual disease (RD; N=37) at surgery following neoadjuvant treatment in the Sammut et al., (2022) cohort.For pCR and RD cases respectively, the percentage of cases (%) is specific according to APOBEC associated COSMIC Reference Signature 2 status (Yes (light green) mutational signature detected in tumour; No (light orange) signature not detected in tumour).(b) Same as (a) but for COSMIC Reference Signature 13.

Supplementary Figure 3. HER2+ subtype specific known breast cancer driver gene list.
Graphical schematic shows the approach used (from left to right) to generate a list of known breast cancer driver genes frequently altered in HER2+ tumour subtype from previously published breast cancer genomic datasets(Rinaldi et al., (2020)andSmith et al., (2021)) for whole exome sequencing data analysis.